A digitally magnified image shows DNA density by varying brightness. There are anywhere from 200 to 300 silica microspheres in each dot. (Source: Lawrence Berkeley National Laboratory)

Detecting specific genes and pathogens in DNA and RNA is typically quite expensive and time consuming. But that's about to change.

Analyzing DNA and RNA -- examining it for things like
certain genes, mutations and pathogens -- has become somewhat more commonplace
in the past few years. One problem is that it requires equipment and expertise
that few of even the best medical centers posses. A group at the Department of
Energy's Lawrence Berkeley Laboratory may change that with their new DNA
microarray analysis technique.

One area of great interest to medical researchers is personalized medicine.
Each person's body reacts differently to diseases, infections, and viruses and
the same can be said for medicines and other treatments. But knowing a person’s
genetic makeup by analyzing their DNA can give treatment specialists insight on
what drug or treatment may work best for a certain individual.

Unfortunately, though the technology exists and works, as mentioned previously,
it presently lies in the hands of a few advanced institutions worldwide.
Fluorescence detection is the most utilized method of DNA analytics, but it
takes specialized equipment and high power devices to implement. Not to mention
time for an analysis to take place.

The Berkeley team's method uses none of these things, instead relying on a
relatively simple approach based on electrostatics. It requires no chemicals
markers, no high energy excitation, and best of all, no microscopes. They boast
that the imaging can be done with nothing more complex than a cell phone camera
if necessary.

They start off with a standard hybridized DNA microarray, set on a positively
charged base. DNA hybridization is a fairly standard technique in which
complementary single strands of DNA combine to form a double-stranded hybrid.
Some DNA will not find complementary strands and will remain single. Then,
after the array is placed in a well chamber, a solution of negatively-charged
silica microspheres is disbursed over the surface of the microarray using
gravitational sedimentation. As the base is positively charged and the
microspheres are negatively charged, the silica spheres will adhere to it in
most places.

The trick is that DNA, hybridized or not, is also negatively charged, with
hybridized segments more so than single strands. This negative charge causes
the silica beads to be repelled and hover above the spots that contain the DNA.
The beads hover at a state of equilibrium based on the repulsion of the
negatively charged DNA samples and the force of gravity. This causes a slightly
frosted look in areas where samples are present, with hybridized samples
standing out more due to the distance of the beads from the surface. Images of
the areas can be analyzed for known genes, mutations or pathogens based on
their charge-density and Brownian motion.

While the technique is much less expensive and complex than fluorescence
detection, the group says they still have room for improvement and intend to
move in that direction. They will be further testing their method on higher
density arrays and experimenting with the absolute limit of resolution
available to the method. Ultimately, it could be used to examine millions of
strands of DNA simultaneously.

This kind of technology could serve to put genetic profiling for medical
purposes like personalized medicine into the hands of doctors in hospitals
worldwide. Rather than relying on a standard treatment, ushering in an era of
personalized medicine may save hundreds of thousands of lives, or more,
world-wide where these blanket treatments are sometimes ineffective. This type
of analytics is looking very promising for the future of medicine, and groups
like Berkeley's are making it more and more possible every day.

"Google fired a shot heard 'round the world, and now a second American company has answered the call to defend the rights of the Chinese people." -- Rep. Christopher H. Smith (R-N.J.)